It has been well documented that the various tubing of a dental unit are covered with a thick biofilm. This biofilm mostly consists of bacteria, but amoebae can be found within the biofilm as well. Some amoebae are potential pathogens and may cause serious infections. Two cases of amoebic infections that were possibly linked with dental units drew our attention and stimulated our researches. Morphologic identification of amoebae in order to determine their possible pathogenicity requires much expertise, and is even difficult for proficient protozoologists. Therefore, the use of PCR is essential to detect potentially pathogenic amoebae with subjectivity. We elaborated new primers for the detection of Acanthamoeba spp. and Naegleria spp. Samples of water and dirt were taken in the environment, and samples of water and biofilm were taken in dental units. A part of each samples was cultivated for morphological identification, when a second part was utilized for PCR identification. Acanthamoebae and/or Naegleriae were detected in 100% of our samples, but the species varied from one sample to another. Potentially pathogenic amoebae were detected in dental units and in the environment, which could represent a health risk for some individuals.